Variant report

Variant	rs1246594
Chromosome Location	chr4:75108571-75108572
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:75108484..75110398-chr4:75159304..75161148,2	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10013212	0.84[EUR][1000 genomes]
rs10017417	0.90[EUR][1000 genomes]
rs10018373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10019396	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs10023519	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10026687	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10433673	0.84[EUR][1000 genomes]
rs10938112	0.84[EUR][1000 genomes]
rs11724468	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs11731340	0.83[EUR][1000 genomes]
rs11737662	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs11942725	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11945418	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1246575	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs1246577	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs1246578	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs1246579	0.97[EUR][1000 genomes]
rs1246580	0.95[EUR][1000 genomes]
rs1246582	0.91[EUR][1000 genomes]
rs1246584	0.91[EUR][1000 genomes]
rs1246586	0.91[EUR][1000 genomes]
rs1246587	0.91[EUR][1000 genomes]
rs1246588	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs1246590	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs1246591	0.85[CEU][hapmap];0.95[EUR][1000 genomes]
rs1246597	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs12500697	0.93[EUR][1000 genomes]
rs1265327	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs13116896	0.84[EUR][1000 genomes]
rs13142241	0.86[EUR][1000 genomes]
rs1371796	0.85[EUR][1000 genomes]
rs1371797	0.80[EUR][1000 genomes]
rs1380561	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs1460016	0.85[EUR][1000 genomes]
rs1460017	0.93[EUR][1000 genomes]
rs16850941	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs17232394	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17829765	1.00[JPT][hapmap]
rs1964526	0.83[EUR][1000 genomes]
rs2045618	0.90[EUR][1000 genomes]
rs2367555	0.84[EUR][1000 genomes]
rs2367745	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs28378517	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28436705	0.84[EUR][1000 genomes]
rs28695994	0.85[EUR][1000 genomes]
rs4371587	0.82[EUR][1000 genomes]
rs4502653	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4577545	0.84[EUR][1000 genomes]
rs4694184	0.89[EUR][1000 genomes]
rs488440	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs536541	0.80[EUR][1000 genomes]
rs565831	0.80[EUR][1000 genomes]
rs62312513	0.91[EUR][1000 genomes]
rs62312515	0.90[EUR][1000 genomes]
rs62312545	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6811214	0.82[EUR][1000 genomes]
rs6821664	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6854203	0.89[EUR][1000 genomes]
rs6854723	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6858809	0.85[EUR][1000 genomes]
rs7670535	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7676371	0.80[EUR][1000 genomes]
rs7678292	0.82[EUR][1000 genomes]
rs7680463	1.00[JPT][hapmap]
rs7681137	0.80[EUR][1000 genomes]
rs7681763	0.80[EUR][1000 genomes]
rs7681912	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs7683181	0.87[EUR][1000 genomes]
rs9992393	0.90[EUR][1000 genomes]
rs9997322	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9997788	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1004768	chr4:74774372-75109579	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1013260	chr4:75013441-75121643	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1002907	chr4:75013441-75131443	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1004706	chr4:75014770-75121643	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1009099	chr4:75089233-75726206	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:75080600-75109600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:75086200-75117600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr4:75093000-75117400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr4:75097400-75117400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:75101400-75117600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr4:75103800-75116400	Weak transcription	NHEK	skin
7	chr4:75108200-75108800	Enhancers	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links